When New York Detective Barbala is thrown through a second story window to his death, the only person in the room is an eight year old girl, Michelle Bishop, whom he was interviewing alone in his office. She claims to have seen another man in the room; the description she gives matches Charlie Morris, a policeman who was murdered by Triads nine years before.

Mulder and Scully head to the girl's home, interviewing her mother Judy Bishop. Michelle's mother tells them that Michelle is disturbed and under psychiatric care. She also gives them information that when her father previously tried to teach her to swim, she would scream upon approaching the water. Michelle's only hobby seems to be the origami figures she makes.

Mulder and Scully question Tony Fiore, Charlie Morris' former partner, he is not very helpful and acts nervous. He tells them he wants to speak outside, not letting them in, because his wife is sleeping inside. He does't go into detail about the murder, saying merely "they just wanted a cop. Any cop." leaving it at that. Hearing them outside, his wife comes out. There is flour on her hands, indicating that he lied about her being asleep. With his wife outside Fiore rushes them out, raising suspicion with both.

When Mulder and Scully leave Fiore goes to former policeman Leon Felder and tells him about the FBI agents' visit. He's anxious that the FBI are connecting the dots; he wants to go to the bank to collect a safety box. Fiore wants to dump it, but Felder is not willing; he wants to keep the money, but Fiore is reluctant. Felder threatens Fiore, pushing that Charlie Morris' death was an accident and that they had merely been trying to scare sense into him. Fiore is clearly uneasy.

Later that night as Leon Felder gets off a bus, an invisible force lifts the back of his scarf trapping it in the bus doors. He calls to the bus driver, who attempts to brake, but cannot. The bus continues to drive against his will, with the driver watching Felder get dragged to his death. He exits the bus in horror, hurrying to the body. As the camera pans in, sitting on the bus a few seats back is Michelle.

Scully and Mulder talk to Michelle's mother in the police station—the woman cries, insisting that Michelle is merely a child and cannot possibly be involved. Mulder, while at the police station, is informed of Felder's past as Barbala's partner when still an officer. Connecting all four police officers to the drug bust, Mulder and Scully dig into their history.

Scully realizes a page is missing from Morris' case file; it was checked out by Fiore that afternoon. They head to his home, where his wife reveals he never came home, before letting the agents in. They ask his wife if she knows Felder or Barbala, but she doesn't recognize the name. Mulder asks about the origami figures he noticed upon entering her home. She reveals that her first husband, Charlie Morris, is the one who made them. The only animal he hadn't finished in his collection was a giraffe.

As they leave, Mulder muses that Michelle was conceived around the time of Morris' death, Scully interrupting him to sarcastically suggest reincarnation. She is not convinced, even with the origami figures, nor the deaths she was witness to. Mulder believes Morris came back to avenge his death, suggesting that she is able to use telekinesis.

Michelle is put into hypnosis, revealing that she is twenty four, before having an attack. She can only get out, "we can't do this, it's wrong" and "they're killing me" before her therapist insists they stop, convincing Michelle's mother that she's in danger of full withdraw. Mulder wants to push forward, but Scully is still unconvinced. She reminds him that even if they get a full recount from Michelle, nothing she says would be admissible, or accepted in court.

Watching back over the tapes that night, Mulder sees an anomaly on the tapes, rewinding it and studying it closer. Upon replay, he can hear a distortion over Michelle's voice, as well as something unusual on the tape itself. Meanwhile Fiore's wife is at home, waiting for news of him when she hears a knock on the door. After rushing to answer it, she finds that an origami giraffe is waiting for her on the porch.

Mulder takes the tape to be studied closer. The analist studying the tapes say whatever image is over Michelle's was with her in the room. Scully receives the autopsy report on Morris' body, revealing that he was actually drowned and mutilated afterwards. The lack of evidence of drowning around his body, except the head and shoulders suggests perhaps he was drowned in a toilet or tub. Scully, looking over his toxicology, deduces that he was actually killed in sea water.

Fiore goes home, calling for his wife frantically. He tells her to pack her bags so they can leave, believing that someone is trying to kill him. Outside of their home, looking into a window is Michelle. Meanwhile the analyst has cleaned up the image on the tape, showing a small underwater diver, which puzzles Scully and the anaylist. However Mulder realizes it must be from the fish tank in Fiore's house, suggesting that Charlie was murdered at home.

Fiore's wife shows him the origami figure, begging to know where it came from when the power suddenly goes off. He tells her to stay in the bedroom while he searches; when he leaves, the door locks, trapping her inside. As he's searching through the house, wire wraps around his legs, knocking him down. He reaches for his gun, but a force drags it away—Michelle appears from the darkness.

Mulder and Scully arrive hearing shattering glass and screaming as they come up to the house. Michelle is using telekenesis to shatter objects around the house, all while remaining expressionless. The agents break into the house through the back door. Fiore tries to speak to Morris, explaining that Felder and Barbala just wanted to talk to him. Fiore wants to know why Morris didn't just take the money.

Michelle attacks, but is stopped by Mulder, who tries to reason with Morris. Morris' wife comes downstairs, hurrying to the fallen Fiore—the man confesses that he knew all along what had been done to Morris, but that he couldn't reveal it. He tells the woman that he just wanted to take care of her; Michelle begins to glow, the fish tank lighting up and shaking as the house starts to break apart.

Morris' wife begs him not to hurt Fiore. The fish tank explodes and the lights come back on.

Mulder narrates as the camera pans to Michelle playing in the pool with her friends. Fiore has gone to jail, charged with Morris' death and extortion. Barbala and Felder's deaths are unsolved, but closed—Michelle is not charged with any crimes, and no longer has any memory of her past life.

Laughing, Howard Gordon revealed "desperation" resulted in Mulder writing the report which concludes this episode. Gordon went on to say, "We had written a scene that was the old wrap-up scene, with the mother looking fondly at her daughter who's now cured of her possession, and we said, 'This is really hokey. This is awful.'" The inclusion of Mulder's journal entry allowed Gordon and Gansa to follow their instinct of understating the paranormal, drily presenting the information. (Cinefantastique, Vol. 26/27, No. 6/1, p. 57)

This episode's script went through six drafts, all of which were submitted in March 1994. One draft was submitted on both 14th and 17th of that month, before two drafts were submitted on 21st, then a single draft on both 22nd and 24th.

Director Jerrold Freedman had fun with the production of this outing. "For episodic television, we had very impressive production values," he mused. "We did some very long steadicam tracking shots and a few other things [....] I found working on 'Born Again' to be an enjoyable experience." (TV Zone issue 81, p. 37)

Due to the swiftness with which Andrea Libman was able to get into character as Michelle Bishop, each of her scenes was shot in only one take. (TV Zone, issue 81, p. 37)

The strongest memory R.W. Goodwin retained from working on this episode was the shooting of its teaser. To film the exterior view of a policeman being propelled through a window in a room which had a pair of side-by-side windows, one of the two windows was made to break easily. "We took out the glass from one of them and put in what we call candy glass," explained Goodwin. "And we used this cannon that blasted the debris out the candy-glass window. We had three or four cameras shooting the thing. They call 'Action', the window blows out, and we realize that the force of the concussion from this cannon has also knocked a hole about three feet across and a foot high in the real window next to our phony window." Key Grip Al Campbell responded to this mistake by making a suggestion. Goodwin continued, "[He] says 'I have a perfect solution for this. When the woman goes to the window, and looks down to see the dead guy, just pan over and next to him will be his dead dog.'" (X-Files Confidential, pp. 74-75)

This episode features the first time that Mulder narrates the story; instead of seeing Scully typing computer reports and hearing her voice-over wrap-up, the audience sees Mulder writing longhand in a field journal and hears his summation of the plot at the episode's conclusion.

A line of dialogue spoken by Mulder in this episode – pertaining to the case of a man who "could influence undeveloped film" and "create shapes on the negative from his mind" – foreshadows the fourth season outing "Unruhe", as well as the characters Ted Serios and Gerry Schnauz therein.

In this episode's teaser, Detective Lazard jokingly tells Detective Barbala he is "a regular Mr. Green Jeans" with children. Lazard is referring to a character from the long-running children's television series Captain Kangaroo, in which Mr. Green Jeans was the sidekick of the series' title character.

When Mulder first informs Scully he suspects Michelle Bishop is a reincarnation of Charlie Morris, Scully makes fun of the postulation by asking Mulder if he believes that, "like Peter Proud," Morris has returned from death to avenge his own murder. This is a reference to the movie The Reincarnation of Peter Proud.

There exists no rail service between Buffalo and its suburbs, including Orchard Park,

Buffalo accents have more in common with Midwestern accents such as Chicago than with New York City, which makes Det. Lazard's accent bizarre.

There is a major medical mistake in this episode. Scully deduces that Morris was drowned in seawater because he had bradycardia (low heart rate) brought on by a sudden increase in sodium levels. While an increase in sodium can cause bradycardia, it is by no means the only thing that can do it. However, the more glaring mistake here is that bradycardia cannot be tested for post-mortem, as it is generally quite difficult to take a dead person's pulse.

Howard Gordon was also dissatisfied with the final version of this installment, believing it to be "a little too cop show-y" for his liking. (The Truth Is Out There: The Official Guide to The X-Files, p. 151) He cited this as his second least favorite episode of the first season, calling it "just mundane." Moments later, Gordon added, "There were parts of it that I think were interesting, but I don't think it was very well executed on any front. It was a pretty classic back-from-the-dead revenge tale, and not done particularly interestingly." However, Gordon described Mulder's narration herein as "interesting" and remarked, "I think that if the episode has anything that recommends it, it's the first time we've heard Mulder's voice talking to the audience. And I think that was actually successful. I liked that wrap-up." (Cinefantastique, Vol. 26/27, No. 6/1, p. 57)

Chris Carter similarly felt this episode was largely dissatisfying though not without some merit. "One of our least successful episodes," he complained. "I thought the direction was a little sloppy, but it's one of those episodes that plays a little closer to reality and I like that about it. There's a nice twist in it about a man marrying the wife of another man he had killed. There were actually some nice effects. Just not one of my favorites." (X-Files Confidential, p. 74)

This episode achieved a Nielsen household rating of 8.2, with an audience share of 14. This means that roughly 8.2 percent of all television-equipped households, and 14 percent of households watching television, were tuned in to the episode. It was viewed by 7.7 million households. These were the third highest viewing figures in The X-Files' first season. (The Truth Is Out There: The Official Guide to The X-Files, p. 248)

Cinefantastique (Vol. 26/27, No. 6/1, p. 57) scores this episode 1 and a half out of 4 stars. The magazine proceeds by stating, "'Born Again' is minor X-Files [....] The villains–corrupt police officers–are possibly the most boring ever on The X-Files and all their scenes are interminable. But even a bad X-Files has its moments; here they are a scene between Mulder and the girl's psychologist, and a sequence where Mulder desperately urges regression hypnosis on the distraught child and Scully chews him out for his obsessive blindness. The scene where an aquarium bursts is very well executed, but in service of a story that fails to ignite." Cinefantastique additionally characterizes this episode as not "great."

In his reference bookWanting to Believe: A Critical Guide to The X-Files, Millennium and The Lone Gunmen, writer Robert Shearman rated this installment 2 and a half out of 5 stars. Shearman criticized this episode as seeming "more generic" but actually "better" than "Roland" and "much more mundane" than "Eve". He went on to remark, "Part of the difficulty is that this wants to be both a telekinesis episode [...] and also a reincarnation episode. Either one of the starting points would have been interesting; to link the two so spuriously makes them both feel a bit woolly, and still doesn't really provide enough meat for forty-five minutes of television [....] What's surprising is how enjoyable this is, never mind how predictable. The set pieces are nicely done [....] And there's a strange quirkiness to the imagery of the episode [...] which make a very ordinary story seem just a little bit extraordinary after all. The characterisation of Mulder and Scully is a little off, perhaps, but it's interesting to see Mulder genuinely rail against Scully for her scepticism. Beyond showing a frustration that may well by now have been shared by a sizeable chunk of the audience, it also suggests the growing tension now that the future of the X-Files feels under threat. Scully gives as good as she gets, though." Shearman also praised Andre Libman's performance as Michelle Bishop, calling it "terrific."